Associated health benefits on mortality of reducing Particulate Matter (PM2.5) in Spain

The objective of the study was to estimate the number of avoidable deaths resulting from reducing ambient air concentrations of PM2.5 in Spain. We used the Community Multiscale Air Quality (CMAQ) model of the U.S. Environmental Protection Agency (EPA) to simulate the levels of air pollution over the whole country corresponding to 2004 -the baseline year- and to estimate the future pollution scenario in 2011 with a reduction in PM2.5 based on air quality policies. To calculate the health impact we used: a) municipal crude mortality rates (all causes, ICD-10: A00-Y98), and population figures of 2004, and b) the concentration-response functions (CRF) based on available epidemiological studies for this health indicator (Pope et al.,2002; Laden et al.,2006). For this purpose, the U.S. EPA´s BenMAP software was used to obtain a global figure of avoidable deaths for the country. According to the simulation, air quality would improve with an average annual reduction of 0.7μg/m 3 in PM2.5 levels. According to Pope’s CRF, this change in PM2.5 levels would imply an annual decline in overall mortality in Spain of 1,718 deaths in the population older than 30 years (6 avoided deaths per 100 000 inhabitants). The total number of deaths in this age range would decrease by 0.5%. According to Laden´s CRF, which restricts the analysis to people between 25-74 years old, the air quality improvement would avoid 1,447 deaths per year. These results show the potential benefits in mortality that could be expected if pollution control policies were successfully implemented in Spai

Blind prediction of homo- and hetero-protein complexes: The CASP13-CAPRI experiment

We present the results for CAPRI Round 46, the third joint CASP-CAPRI protein assembly prediction challenge. The Round comprised a total of 20 targets including 14 homo-oligomers and 6 heterocomplexes. Eight of the homo-oligomer targets and one heterodimer comprised proteins that could be readily modeled using templates from the Protein Data Bank, often available for the full assembly. The remaining 11 targets comprised 5 homodimers, 3 heterodimers, and two higher-order assemblies. These were more difficult to model, as their prediction mainly involved “ab-initio” docking of subunit models derived from distantly related templates. A total of ~30 CAPRI groups, including 9 automatic servers, submitted on average ~2000 models per target. About 17 groups participated in the CAPRI scoring rounds, offered for most targets, submitting ~170 models per target. The prediction performance, measured by the fraction of models of acceptable quality or higher submitted across all predictors groups, was very good to excellent for the nine easy targets. Poorer performance was achieved by predictors for the 11 difficult targets, with medium and high quality models submitted for only 3 of these targets. A similar performance “gap” was displayed by scorer groups, highlighting yet again the unmet challenge of modeling the conformational changes of the protein components that occur upon binding or that must be accounted for in template-based modeling. Our analysis also indicates that residues in binding interfaces were less well predicted in this set of targets than in previous Rounds, providing useful insights for directions of future improvements

Prediction of protein assemblies, the next frontier: The CASP14-CAPRI experiment

We present the results for CAPRI Round 50, the fourth joint CASP-CAPRI protein assembly prediction challenge. The Round comprised a total of twelve targets, including six dimers, three trimers, and three higher-order oligomers. Four of these were easy targets, for which good structural templates were available either for the full assembly, or for the main interfaces (of the higher-order oligomers). Eight were difficult targets for which only distantly related templates were found for the individual subunits. Twenty-five CAPRI groups including eight automatic servers submitted ~1250 models per target. Twenty groups including six servers participated in the CAPRI scoring challenge submitted ~190 models per target. The accuracy of the predicted models was evaluated using the classical CAPRI criteria. The prediction performance was measured by a weighted scoring scheme that takes into account the number of models of acceptable quality or higher submitted by each group as part of their five top-ranking models. Compared to the previous CASP-CAPRI challenge, top performing groups submitted such models for a larger fraction (70–75%) of the targets in this Round, but fewer of these models were of high accuracy. Scorer groups achieved stronger performance with more groups submitting correct models for 70–80% of the targets or achieving high accuracy predictions. Servers performed less well in general, except for the MDOCKPP and LZERD servers, who performed on par with human groups. In addition to these results, major advances in methodology are discussed, providing an informative overview of where the prediction of protein assemblies currently stands